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    You may be aware of PHPUnit part of PEAR, there is also another package called phpDocumentor, which forms a description document for the PHP you are working on.
I have just run it on Xortify and I have around 6000 errors by the core developers in malformed or missing commenting.
When commenting the top of the file is something like:
 /** 
 * XOOPS Authentification base class 
 * 
 * You may not change or alter any portion of this comment or credits 
 * of supporting developers from this source code or any supporting source code 
 * which is considered copyrighted (c) material of the original comment or credit authors. 
 * This program is distributed in the hope that it will be useful, 
 * but WITHOUT ANY WARRANTY; without even the implied warranty of 
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
 * 
 * @copyright       Chronolabs Coopertive (Australia)  http://web.labs.coop 
 * @license         GNU GPL 2 (http://www.gnu.org/licenses/old-licenses/gpl-2.0.html) 
 * @package         kernel 
 * @subpackage      auth 
 * @since           2.0 
 * @author          Pierre-Eric MENUET  
 * @version         $Id: auth.php 8066 2011-11-06 05:09:33Z beckmi $ 
 */  At the top of a class it has to contain a summary like so (the summary is the first lines with no @ ie 'Authentification base class'):
 /**  
 * Authentification base class 
 * 
 * @package kernel 
 * @subpackage auth 
 * @description Authentification base class 
 * @author Pierre-Eric MENUET  
 * @copyright copyright (c) 2000-2003 XOOPS.org 
 */  All Variables have to be done like so:
 /** 
     * Database Property 
     */ 
    var $_dao;  
ANd functions like propertys like variables in classes and functions are commented like so:
 /** 
     * Authentication of a User 
     * 
     * @abstract need to be write in the dervied class 
     */ 
    function authenticate() 
    { 
        $authenticated = false; 
 
        return $authenticated; 
    }  
This file i have used as and example is fixing the issues surrounding running phpDocumentor (which is what they built the original PHP.NET sites from) on the file htdocs/class/auth/auth.php
If you would and I hope fix this issues so I don't as I do now have to go through and fix all the commenting so i have clean PHPDocuments.. I have left a copy of the dismal 8000 commenting errors copy here for a guide of where and what comments need to be fixed 
http://devl.labs.coop/2.6.0%20a3/